Package Recipe 'cnv_facets'

recipe cnv_facets

Detect somatic copy number variants (CNV) in tumour-normal samples using next generation sequencing data

Homepage:: https://github.com/dariober/cnv_facets
License:: MIT / MIT
Recipe:: /cnv_facets/meta.yaml

package cnv_facets¶

Versions:

0.16.1-1, 0.16.1-0, 0.16.0-1, 0.16.0-0, 0.15.0-1, 0.15.0-0, 0.14.0-1, 0.13.0-1, 0.12.1-1,

0.16.1-1, 0.16.1-0, 0.16.0-1, 0.16.0-0, 0.15.0-1, 0.15.0-0, 0.14.0-1, 0.13.0-1, 0.12.1-1, 0.12.1-0, 0.12.0-0, v0.11.3-2, v0.11.3-1, v0.11.2-1

Depends:

on bcftools >=1.21,<2.0a0
on bcftools >=1.9
on bioconductor-rsamtools >=2.18.0,<2.19.0a0
on htslib >=1.21,<1.24.0a0
on libgcc >=12
on libgfortran
on libgfortran5 >=12.4.0
on libstdcxx >=12
on python >=3.12,<3.13.0a0
on r-argparse >=2.1.6
on r-base >=4.3,<4.4.0a0
on r-data.table
on r-facets >=0.6.2,<1.0a0
on r-ggplot2
on r-gridextra
on r-jsonlite
on samtools >=1.21,<2.0a0
on snp-pileup >=0.6.2,<0.7.0a0

Additional platforms:

linux-aarch64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install cnv_facets

to add into an existing workspace instead, run:

pixi add cnv_facets

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install cnv_facets

Alternatively, to install into a new environment, run:

conda create -n envname cnv_facets

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/cnv_facets:<tag>

(see cnv_facets/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/cnv_facets/README.html)